Re: [gmx-users] Define intermolecular interactions in L-J simulation
> > > Den 2019-10-23 kl. 18:22, skrev Li, Shi: > > Dear GMX users, > > > > I am wondering if there is a way to define the intermolecular interaction > > to simulation a binary LJ system. For example, I have two atoms A and B, > > they share the same LJ parameter, and I want to change the interaction > > parameter between A and B, so that I would expect different behaviors > from > > the simulation (mix or phase separation). > > > > I checked the manual and found this can be defined in the topology file > as > > [intermolecular_interactions] and use the [pairs] interaction then list > the > > atom pairs. But it is still confusing if I have a system containing 500 A > > and 500 B, how can I apply this to the entire binary system. I was > > assumed that I can use atomtype instead of atom number? But how and where > > to specify that? > > > > Any suggestions? > > > > Thanks, > > Shi > > > Use > [ nonbonded_types ] > A A 1 c6 c12 > B B 1 c6 c12 > A B 1 c6 c12 > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > > > Thank you so much! This works very well. Shi > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Define intermolecular interactions in L-J simulation
Den 2019-10-23 kl. 18:22, skrev Li, Shi: Dear GMX users, I am wondering if there is a way to define the intermolecular interaction to simulation a binary LJ system. For example, I have two atoms A and B, they share the same LJ parameter, and I want to change the interaction parameter between A and B, so that I would expect different behaviors from the simulation (mix or phase separation). I checked the manual and found this can be defined in the topology file as [intermolecular_interactions] and use the [pairs] interaction then list the atom pairs. But it is still confusing if I have a system containing 500 A and 500 B, how can I apply this to the entire binary system. I was assumed that I can use atomtype instead of atom number? But how and where to specify that? Any suggestions? Thanks, Shi Use [ nonbonded_types ] A A 1 c6 c12 B B 1 c6 c12 A B 1 c6 c12 -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Define intermolecular interactions in L-J simulation
On 10/23/19 12:22 PM, Li, Shi wrote: Dear GMX users, I am wondering if there is a way to define the intermolecular interaction to simulation a binary LJ system. For example, I have two atoms A and B, they share the same LJ parameter, and I want to change the interaction parameter between A and B, so that I would expect different behaviors from the simulation (mix or phase separation). I checked the manual and found this can be defined in the topology file as [intermolecular_interactions] and use the [pairs] interaction then list the [intermolecular_interactions] are for bonded interactions and [pairs] are for 1-4 interactions. atom pairs. But it is still confusing if I have a system containing 500 A and 500 B, how can I apply this to the entire binary system. I was assumed that I can use atomtype instead of atom number? But how and where to specify that? It sounds like you want to override combination rules, in which case you want [nonbond_params] to create an off-diagonal LJ interaction. A and B need to be defined as different atom types but can have the same LJ so A-A and B-B interactions obey the combination rule but A-B can be whatever you want it to be. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Define intermolecular interactions in L-J simulation
Dear GMX users, I am wondering if there is a way to define the intermolecular interaction to simulation a binary LJ system. For example, I have two atoms A and B, they share the same LJ parameter, and I want to change the interaction parameter between A and B, so that I would expect different behaviors from the simulation (mix or phase separation). I checked the manual and found this can be defined in the topology file as [intermolecular_interactions] and use the [pairs] interaction then list the atom pairs. But it is still confusing if I have a system containing 500 A and 500 B, how can I apply this to the entire binary system. I was assumed that I can use atomtype instead of atom number? But how and where to specify that? Any suggestions? Thanks, Shi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
